Documentation Index

This directory contains comprehensive documentation for the SciTeX Writer template system. Files are organized with explicit descriptive prefixes for semantic clarity and easy navigation.

Main Documentation (Root Level)

Guides (01_GUIDE_*)

Procedural documentation for common tasks and workflows:
- 01_GUIDE_QUICK_START.md - Quick reference for common tasks and basic workflows
- 01_GUIDE_INSTALLATION.md - Setup for all environments
- 01_GUIDE_BIBLIOGRAPHY.md - Complete guide to bibliography management with multi-file support and caching
- 01_GUIDE_CONTENT_CREATION.md - Comprehensive guide for creating and managing figures and tables
- 01_GUIDE_AGENTS.md - Guide for using AI agents and LLMs with the system

Architecture (02_ARCHITECTURE_*)

Technical design and implementation details:
- 02_ARCHITECTURE_IMPLEMENTATION.md - System architecture, technical implementation, and troubleshooting guide

MCP Tools

• MCP_TOOLS.md - Reference for all 29 MCP tools for AI agent integration

Subdirectories

to_claude/

Configuration and guidelines for Claude Code integration:
- agents/ - Individual agent specifications and responsibilities
- bin/ - Utility scripts and tools
- examples/ - Example projects and workflows
- guidelines/ - Development guidelines organized by topic:
- command/ - Command reference guides
- elisp/ - Emacs Lisp development standards
- programming_common/ - General programming best practices
- project/ - Project-level standards
- python/ - Python-specific guidelines
- science/ - Scientific writing standards
- shell/ - Shell scripting guidelines

INSTRUCTIONS_TO_CLAUDE_CODE/

Step-by-step instructions for Claude Code tasks:
- Custom Python management
- Project structure guidelines
- Testing strategies
- Shell scripting
- Git/GitHub workflows
- System information and troubleshooting

structure/

• structure.md - Directory structure documentation
• structure.mmd - Mermaid diagram of repository structure

Navigation Tips

1. For quick answers: Start with 01_GUIDE_QUICK_START.md
2. For installation: See 01_GUIDE_INSTALLATION.md
3. For bibliography management: See 01_GUIDE_BIBLIOGRAPHY.md
4. For figure/table creation: See 01_GUIDE_CONTENT_CREATION.md
5. For AI agent and LLM setup: Consult 01_GUIDE_AGENTS.md
6. For technical architecture: Review 02_ARCHITECTURE_IMPLEMENTATION.md
7. For MCP tools reference: See MCP_TOOLS.md
8. For Python development: Check to_claude/guidelines/python/ directory
9. For project management: Look in to_claude/guidelines/project/
10. For scientific writing standards: See to_claude/guidelines/science/ directory

File Naming Convention

Root-level documentation files use explicit descriptive prefixes for semantic meaning:

• 01_GUIDE_* = Guide (procedural, how-to documentation)
• 01_GUIDE_QUICK_START.md - Quick reference for immediate needs
• 01_GUIDE_INSTALLATION.md - Setup for all environments
• 01_GUIDE_BIBLIOGRAPHY.md - Bibliography management and organization
• 01_GUIDE_CONTENT_CREATION.md - Detailed creation processes

• 01_GUIDE_AGENTS.md - AI and LLM integration

• 02_ARCHITECTURE_* = Architecture (technical design and implementation)

• 02_ARCHITECTURE_IMPLEMENTATION.md - System design and technical details

This prefix system provides immediate visual context about document purpose and category when viewing directory listings.

Subdirectory files within to_claude/guidelines/ use numbered prefixes when they represent sequential steps or priority levels (e.g., 01_DEVELOPMENT_CYCLE.md, 02_NAMING_CONVENSIONS.md).